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- PDB-4ggv: Crystal Structure of HmtT Involved in Himastatin Biosynthesis -

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Basic information

Entry
Database: PDB / ID: 4ggv
TitleCrystal Structure of HmtT Involved in Himastatin Biosynthesis
ComponentsCytochrome P450 superfamily protein
KeywordsOXIDOREDUCTASE / Cysteine-ligand loop / Hydrolase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 superfamily protein
Similarity search - Component
Biological speciesStreptomyces himastatinicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.331 Å
AuthorsZhang, H. / Chen, J. / Wang, H. / Zhang, H.
CitationJournal: Febs Lett. / Year: 2013
Title: Structural analysis of HmtT and HmtN involved in the tailoring steps of himastatin biosynthesis
Authors: Zhang, H. / Chen, J. / Wang, H. / Xie, Y. / Ju, J. / Yan, Y. / Zhang, H.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0942
Polymers46,4771
Non-polymers6161
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 121.139, 54.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

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Components

#1: Protein Cytochrome P450 superfamily protein / Putative P450-like enzyme


Mass: 46477.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces himastatinicus (bacteria) / Strain: ATCC 53653 / Gene: hmtT, SSOG_07642 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D9WMR2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8%(w/v) PEG4000, 3%(v/v) Dimethyl Sulfoxide, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979228 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 2.331→44.1244 Å / Num. all: 18771 / Num. obs: 17864 / % possible obs: 99.9578 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.4 / Redundancy: 4.3 % / Biso Wilson estimate: 24.89 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.331→2.37 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJO

2jjo


Resolution: 2.331→44.124 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 913 5.11 %
Rwork0.2076 --
all0.2214 18777 -
obs0.2102 17864 94.27 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.525 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0496 Å2-0 Å20 Å2
2---1.6763 Å2-0 Å2
3---4.726 Å2
Refinement stepCycle: LAST / Resolution: 2.331→44.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 43 150 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053223
X-RAY DIFFRACTIONf_angle_d0.9314416
X-RAY DIFFRACTIONf_dihedral_angle_d13.9941190
X-RAY DIFFRACTIONf_chiral_restr0.065495
X-RAY DIFFRACTIONf_plane_restr0.004584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.331-2.45350.32461050.228180072
2.4535-2.60720.29151430.2303233193
2.6072-2.80840.3221350.23492525100
2.8084-3.0910.32681320.22492537100
3.091-3.53810.24891390.21532530100
3.5381-4.4570.2131330.1772258499
4.457-44.13230.21351260.1999264496

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